Question: Which read counts file from miRDeep2 should be considered for differential expression analysis?
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3.3 years ago by
United States
bioinforesearchquestions280 wrote:

Hello everyone,

I would appreciate some help with my data. I want to do Differential Expression profiling for miRNA samples.

Using the miRDeep2 program and algorithm, I'm in trouble when dealing with results to make a proper table in order to use it as input for DE software such as EdgeR or DEseq2.

Which .csv should be used for read count?




Also, there are duplicate values in the miRNA_expressed.csv. Should I consider the average or only one of them with highest value?

miRNA read_count precursor

ssc-let-7a 66271 ssc-let-7a-1

ssc-let-7a 66388 ssc-let-7a-2

ssc-let-7c 22747 ssc-let-7c

mirna rna-seq mirdeep2 mirbase • 2.1k views
ADD COMMENTlink modified 3.2 years ago by h.mon32k • written 3.3 years ago by bioinforesearchquestions280
gravatar for h.mon
3.2 years ago by
h.mon32k wrote:

You should use the miRNAs_expressed_all_samples_15_09_2017_t_07_26_27.csv as input for edgeR or DESeq.

miDeep2 runs bowtie with -a (report all alignments) and --best --strata, which means the same read will be mapped to multiple precursor miRNAs, so I believe you should use only one of the counts for each mature miRNA - I would use the one with higher counts.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by h.mon32k
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